See [http://bugzilla.open-bio.org/show_bug.cgi?id=2837 Bug 2837], based on code from Jose Blanca.

+

See [http://bugzilla.open-bio.org/show_bug.cgi?id=2837 Bug 2837], based on code from Jose Blanca. Recently merged into the trunk and should be included in Biopython 1.54 onwards.

=== Open Enhancement Bugs ===

=== Open Enhancement Bugs ===

Revision as of 13:34, 25 February 2010

This page provides a central location to collect references to active projects. This is a good place to start if you are interested in contributing to Biopython and want to find larger projects in progress. For developers, use this to reference git branches or other projects which you will be working on for an extended period of time. Please keep it up to date as projects are finished and integrated into Biopython.

Phylo

Eric is working on a new module for phylogenetics, Bio.Phylo. It grew out of a Google Summer of Code 2009 project, mentored by Brad, to add support for phyloXML to Biopython; it also refactors part of Bio.Nexus. Most of the code has been pushed to the main development branch on GitHub already, but new features appear first on Eric's phyloxml branch.

Use SQLAlchemy, an object relational mapper, for BioSQL internals. This would add an additional external dependency to Biopython, but provides ready support for additional databases like SQLite. It also would provide a raw object interface to BioSQL databases when the SeqRecord-like interface is not sufficient. Brad and Kyle have some initial code for this.

Enhancement list

Maintaining software involves incremental improvements for new format changes and removal of bugs. Please see our bugzilla page for a current list. Post to the developer mailing list if you are interested in tackling any open issues.